Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping

Grain length (GL) directly affects the yield and quality of rice. Very few cloned GL-related genes are applied in production because their yield-increasing effects are not obvious, and the overall regulatory networks underlying the associated processes remain poorly understood. DNA samples from two...
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Autor*in:	Lan Wang [verfasserIn] Yang Liu [verfasserIn] Haiyan Zhao [verfasserIn] Yuebin Zheng [verfasserIn] Feng Bai [verfasserIn] Sicheng Deng [verfasserIn] Zhixiong Chen [verfasserIn] Jinwen Wu [verfasserIn] Xiangdong Liu [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2022

Schlagwörter:	wild rice grain length BSA fine mapping gene cloning

Übergeordnetes Werk:	In: Frontiers in Plant Science - Frontiers Media S.A., 2011, 13(2022)
Übergeordnetes Werk:	volume:13 ; year:2022

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3389/fpls.2022.921029

Katalog-ID:	DOAJ041626680

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allfields	10.3389/fpls.2022.921029 doi (DE-627)DOAJ041626680 (DE-599)DOAJe359d4fc4f954e16825ceee832e46e6a DE-627 ger DE-627 rakwb eng SB1-1110 Lan Wang verfasserin aut Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Grain length (GL) directly affects the yield and quality of rice. Very few cloned GL-related genes are applied in production because their yield-increasing effects are not obvious, and the overall regulatory networks underlying the associated processes remain poorly understood. DNA samples from two bulk DNA pools (L-pool and S-pool) and their parents (KJ01 and Huaye 3) were subjected to high-throughput sequencing. Using bulked segregant analysis (BSA), qGL3.5 was mapped to a 0.34-Mb “hotspot” region on chromosome 3 that contains 37 genes related to various traits. Then, qGL3.5 was mapped to the genomic interval between the flanking markers M2 and M3 using 2786 BC4F2 individuals. Because the region from B5 to B6 was not the associated region under BSA-seq analysis, qGL3.5 was narrowed down to the interval between B6 and M3, which spanned 24.0-kb. Of all 37 genes with non-synonymous single-nucleotide polymorphisms (SNPs) between KJ01 and Huaye 3 based on BSA-seq analysis, only one complete annotated gene, ORF18 (Gene ID: LOC_Os03g42790.1) was found. ORF18 encodes an IBR-RING zinc-finger-related protein, with one really interesting new gene (RING) and two in between ring finger (IBR) domains. The knockout of ORF18 derived from Huaye 3 using clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) editing technology increased the GL of the mutant by approximately 2.2 mm. The novel locus qGL3.5 negatively regulated GL by promoting elongation of the longitudinal cell of the grain outer glume. These results provide a new genetic resource for rice grain shape breeding and a starting point for the functional characterization of the wild rice GL gene. wild rice grain length BSA fine mapping gene cloning Plant culture Lan Wang verfasserin aut Lan Wang verfasserin aut Yang Liu verfasserin aut Yang Liu verfasserin aut Yang Liu verfasserin aut Haiyan Zhao verfasserin aut Haiyan Zhao verfasserin aut Yuebin Zheng verfasserin aut Yuebin Zheng verfasserin aut Yuebin Zheng verfasserin aut Feng Bai verfasserin aut Feng Bai verfasserin aut Feng Bai verfasserin aut Sicheng Deng verfasserin aut Zhixiong Chen verfasserin aut Zhixiong Chen verfasserin aut Zhixiong Chen verfasserin aut Jinwen Wu verfasserin aut Jinwen Wu verfasserin aut Jinwen Wu verfasserin aut Xiangdong Liu verfasserin aut Xiangdong Liu verfasserin aut Xiangdong Liu verfasserin aut In Frontiers in Plant Science Frontiers Media S.A., 2011 13(2022) (DE-627)662359240 (DE-600)2613694-6 1664462X nnns volume:13 year:2022 https://doi.org/10.3389/fpls.2022.921029 kostenfrei https://doaj.org/article/e359d4fc4f954e16825ceee832e46e6a kostenfrei https://www.frontiersin.org/articles/10.3389/fpls.2022.921029/full kostenfrei https://doaj.org/toc/1664-462X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2022
spelling	10.3389/fpls.2022.921029 doi (DE-627)DOAJ041626680 (DE-599)DOAJe359d4fc4f954e16825ceee832e46e6a DE-627 ger DE-627 rakwb eng SB1-1110 Lan Wang verfasserin aut Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Grain length (GL) directly affects the yield and quality of rice. Very few cloned GL-related genes are applied in production because their yield-increasing effects are not obvious, and the overall regulatory networks underlying the associated processes remain poorly understood. DNA samples from two bulk DNA pools (L-pool and S-pool) and their parents (KJ01 and Huaye 3) were subjected to high-throughput sequencing. Using bulked segregant analysis (BSA), qGL3.5 was mapped to a 0.34-Mb “hotspot” region on chromosome 3 that contains 37 genes related to various traits. Then, qGL3.5 was mapped to the genomic interval between the flanking markers M2 and M3 using 2786 BC4F2 individuals. Because the region from B5 to B6 was not the associated region under BSA-seq analysis, qGL3.5 was narrowed down to the interval between B6 and M3, which spanned 24.0-kb. Of all 37 genes with non-synonymous single-nucleotide polymorphisms (SNPs) between KJ01 and Huaye 3 based on BSA-seq analysis, only one complete annotated gene, ORF18 (Gene ID: LOC_Os03g42790.1) was found. ORF18 encodes an IBR-RING zinc-finger-related protein, with one really interesting new gene (RING) and two in between ring finger (IBR) domains. The knockout of ORF18 derived from Huaye 3 using clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) editing technology increased the GL of the mutant by approximately 2.2 mm. The novel locus qGL3.5 negatively regulated GL by promoting elongation of the longitudinal cell of the grain outer glume. These results provide a new genetic resource for rice grain shape breeding and a starting point for the functional characterization of the wild rice GL gene. wild rice grain length BSA fine mapping gene cloning Plant culture Lan Wang verfasserin aut Lan Wang verfasserin aut Yang Liu verfasserin aut Yang Liu verfasserin aut Yang Liu verfasserin aut Haiyan Zhao verfasserin aut Haiyan Zhao verfasserin aut Yuebin Zheng verfasserin aut Yuebin Zheng verfasserin aut Yuebin Zheng verfasserin aut Feng Bai verfasserin aut Feng Bai verfasserin aut Feng Bai verfasserin aut Sicheng Deng verfasserin aut Zhixiong Chen verfasserin aut Zhixiong Chen verfasserin aut Zhixiong Chen verfasserin aut Jinwen Wu verfasserin aut Jinwen Wu verfasserin aut Jinwen Wu verfasserin aut Xiangdong Liu verfasserin aut Xiangdong Liu verfasserin aut Xiangdong Liu verfasserin aut In Frontiers in Plant Science Frontiers Media S.A., 2011 13(2022) (DE-627)662359240 (DE-600)2613694-6 1664462X nnns volume:13 year:2022 https://doi.org/10.3389/fpls.2022.921029 kostenfrei https://doaj.org/article/e359d4fc4f954e16825ceee832e46e6a kostenfrei https://www.frontiersin.org/articles/10.3389/fpls.2022.921029/full kostenfrei https://doaj.org/toc/1664-462X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2022
allfields_unstemmed	10.3389/fpls.2022.921029 doi (DE-627)DOAJ041626680 (DE-599)DOAJe359d4fc4f954e16825ceee832e46e6a DE-627 ger DE-627 rakwb eng SB1-1110 Lan Wang verfasserin aut Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Grain length (GL) directly affects the yield and quality of rice. Very few cloned GL-related genes are applied in production because their yield-increasing effects are not obvious, and the overall regulatory networks underlying the associated processes remain poorly understood. DNA samples from two bulk DNA pools (L-pool and S-pool) and their parents (KJ01 and Huaye 3) were subjected to high-throughput sequencing. Using bulked segregant analysis (BSA), qGL3.5 was mapped to a 0.34-Mb “hotspot” region on chromosome 3 that contains 37 genes related to various traits. Then, qGL3.5 was mapped to the genomic interval between the flanking markers M2 and M3 using 2786 BC4F2 individuals. Because the region from B5 to B6 was not the associated region under BSA-seq analysis, qGL3.5 was narrowed down to the interval between B6 and M3, which spanned 24.0-kb. Of all 37 genes with non-synonymous single-nucleotide polymorphisms (SNPs) between KJ01 and Huaye 3 based on BSA-seq analysis, only one complete annotated gene, ORF18 (Gene ID: LOC_Os03g42790.1) was found. ORF18 encodes an IBR-RING zinc-finger-related protein, with one really interesting new gene (RING) and two in between ring finger (IBR) domains. The knockout of ORF18 derived from Huaye 3 using clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) editing technology increased the GL of the mutant by approximately 2.2 mm. The novel locus qGL3.5 negatively regulated GL by promoting elongation of the longitudinal cell of the grain outer glume. These results provide a new genetic resource for rice grain shape breeding and a starting point for the functional characterization of the wild rice GL gene. wild rice grain length BSA fine mapping gene cloning Plant culture Lan Wang verfasserin aut Lan Wang verfasserin aut Yang Liu verfasserin aut Yang Liu verfasserin aut Yang Liu verfasserin aut Haiyan Zhao verfasserin aut Haiyan Zhao verfasserin aut Yuebin Zheng verfasserin aut Yuebin Zheng verfasserin aut Yuebin Zheng verfasserin aut Feng Bai verfasserin aut Feng Bai verfasserin aut Feng Bai verfasserin aut Sicheng Deng verfasserin aut Zhixiong Chen verfasserin aut Zhixiong Chen verfasserin aut Zhixiong Chen verfasserin aut Jinwen Wu verfasserin aut Jinwen Wu verfasserin aut Jinwen Wu verfasserin aut Xiangdong Liu verfasserin aut Xiangdong Liu verfasserin aut Xiangdong Liu verfasserin aut In Frontiers in Plant Science Frontiers Media S.A., 2011 13(2022) (DE-627)662359240 (DE-600)2613694-6 1664462X nnns volume:13 year:2022 https://doi.org/10.3389/fpls.2022.921029 kostenfrei https://doaj.org/article/e359d4fc4f954e16825ceee832e46e6a kostenfrei https://www.frontiersin.org/articles/10.3389/fpls.2022.921029/full kostenfrei https://doaj.org/toc/1664-462X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2022
allfieldsGer	10.3389/fpls.2022.921029 doi (DE-627)DOAJ041626680 (DE-599)DOAJe359d4fc4f954e16825ceee832e46e6a DE-627 ger DE-627 rakwb eng SB1-1110 Lan Wang verfasserin aut Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Grain length (GL) directly affects the yield and quality of rice. Very few cloned GL-related genes are applied in production because their yield-increasing effects are not obvious, and the overall regulatory networks underlying the associated processes remain poorly understood. DNA samples from two bulk DNA pools (L-pool and S-pool) and their parents (KJ01 and Huaye 3) were subjected to high-throughput sequencing. Using bulked segregant analysis (BSA), qGL3.5 was mapped to a 0.34-Mb “hotspot” region on chromosome 3 that contains 37 genes related to various traits. Then, qGL3.5 was mapped to the genomic interval between the flanking markers M2 and M3 using 2786 BC4F2 individuals. Because the region from B5 to B6 was not the associated region under BSA-seq analysis, qGL3.5 was narrowed down to the interval between B6 and M3, which spanned 24.0-kb. Of all 37 genes with non-synonymous single-nucleotide polymorphisms (SNPs) between KJ01 and Huaye 3 based on BSA-seq analysis, only one complete annotated gene, ORF18 (Gene ID: LOC_Os03g42790.1) was found. ORF18 encodes an IBR-RING zinc-finger-related protein, with one really interesting new gene (RING) and two in between ring finger (IBR) domains. The knockout of ORF18 derived from Huaye 3 using clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) editing technology increased the GL of the mutant by approximately 2.2 mm. The novel locus qGL3.5 negatively regulated GL by promoting elongation of the longitudinal cell of the grain outer glume. These results provide a new genetic resource for rice grain shape breeding and a starting point for the functional characterization of the wild rice GL gene. wild rice grain length BSA fine mapping gene cloning Plant culture Lan Wang verfasserin aut Lan Wang verfasserin aut Yang Liu verfasserin aut Yang Liu verfasserin aut Yang Liu verfasserin aut Haiyan Zhao verfasserin aut Haiyan Zhao verfasserin aut Yuebin Zheng verfasserin aut Yuebin Zheng verfasserin aut Yuebin Zheng verfasserin aut Feng Bai verfasserin aut Feng Bai verfasserin aut Feng Bai verfasserin aut Sicheng Deng verfasserin aut Zhixiong Chen verfasserin aut Zhixiong Chen verfasserin aut Zhixiong Chen verfasserin aut Jinwen Wu verfasserin aut Jinwen Wu verfasserin aut Jinwen Wu verfasserin aut Xiangdong Liu verfasserin aut Xiangdong Liu verfasserin aut Xiangdong Liu verfasserin aut In Frontiers in Plant Science Frontiers Media S.A., 2011 13(2022) (DE-627)662359240 (DE-600)2613694-6 1664462X nnns volume:13 year:2022 https://doi.org/10.3389/fpls.2022.921029 kostenfrei https://doaj.org/article/e359d4fc4f954e16825ceee832e46e6a kostenfrei https://www.frontiersin.org/articles/10.3389/fpls.2022.921029/full kostenfrei https://doaj.org/toc/1664-462X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2022
allfieldsSound	10.3389/fpls.2022.921029 doi (DE-627)DOAJ041626680 (DE-599)DOAJe359d4fc4f954e16825ceee832e46e6a DE-627 ger DE-627 rakwb eng SB1-1110 Lan Wang verfasserin aut Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Grain length (GL) directly affects the yield and quality of rice. Very few cloned GL-related genes are applied in production because their yield-increasing effects are not obvious, and the overall regulatory networks underlying the associated processes remain poorly understood. DNA samples from two bulk DNA pools (L-pool and S-pool) and their parents (KJ01 and Huaye 3) were subjected to high-throughput sequencing. Using bulked segregant analysis (BSA), qGL3.5 was mapped to a 0.34-Mb “hotspot” region on chromosome 3 that contains 37 genes related to various traits. Then, qGL3.5 was mapped to the genomic interval between the flanking markers M2 and M3 using 2786 BC4F2 individuals. Because the region from B5 to B6 was not the associated region under BSA-seq analysis, qGL3.5 was narrowed down to the interval between B6 and M3, which spanned 24.0-kb. Of all 37 genes with non-synonymous single-nucleotide polymorphisms (SNPs) between KJ01 and Huaye 3 based on BSA-seq analysis, only one complete annotated gene, ORF18 (Gene ID: LOC_Os03g42790.1) was found. ORF18 encodes an IBR-RING zinc-finger-related protein, with one really interesting new gene (RING) and two in between ring finger (IBR) domains. The knockout of ORF18 derived from Huaye 3 using clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) editing technology increased the GL of the mutant by approximately 2.2 mm. The novel locus qGL3.5 negatively regulated GL by promoting elongation of the longitudinal cell of the grain outer glume. These results provide a new genetic resource for rice grain shape breeding and a starting point for the functional characterization of the wild rice GL gene. wild rice grain length BSA fine mapping gene cloning Plant culture Lan Wang verfasserin aut Lan Wang verfasserin aut Yang Liu verfasserin aut Yang Liu verfasserin aut Yang Liu verfasserin aut Haiyan Zhao verfasserin aut Haiyan Zhao verfasserin aut Yuebin Zheng verfasserin aut Yuebin Zheng verfasserin aut Yuebin Zheng verfasserin aut Feng Bai verfasserin aut Feng Bai verfasserin aut Feng Bai verfasserin aut Sicheng Deng verfasserin aut Zhixiong Chen verfasserin aut Zhixiong Chen verfasserin aut Zhixiong Chen verfasserin aut Jinwen Wu verfasserin aut Jinwen Wu verfasserin aut Jinwen Wu verfasserin aut Xiangdong Liu verfasserin aut Xiangdong Liu verfasserin aut Xiangdong Liu verfasserin aut In Frontiers in Plant Science Frontiers Media S.A., 2011 13(2022) (DE-627)662359240 (DE-600)2613694-6 1664462X nnns volume:13 year:2022 https://doi.org/10.3389/fpls.2022.921029 kostenfrei https://doaj.org/article/e359d4fc4f954e16825ceee832e46e6a kostenfrei https://www.frontiersin.org/articles/10.3389/fpls.2022.921029/full kostenfrei https://doaj.org/toc/1664-462X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2022
language	English
source	In Frontiers in Plant Science 13(2022) volume:13 year:2022
sourceStr	In Frontiers in Plant Science 13(2022) volume:13 year:2022
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	wild rice grain length BSA fine mapping gene cloning Plant culture
isfreeaccess_bool	true
container_title	Frontiers in Plant Science
authorswithroles_txt_mv	Lan Wang @@aut@@ Yang Liu @@aut@@ Haiyan Zhao @@aut@@ Yuebin Zheng @@aut@@ Feng Bai @@aut@@ Sicheng Deng @@aut@@ Zhixiong Chen @@aut@@ Jinwen Wu @@aut@@ Xiangdong Liu @@aut@@
publishDateDaySort_date	2022-01-01T00:00:00Z
hierarchy_top_id	662359240
id	DOAJ041626680
language_de	englisch
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callnumber-first	S - Agriculture
author	Lan Wang
spellingShingle	Lan Wang misc SB1-1110 misc wild rice misc grain length misc BSA misc fine mapping misc gene cloning misc Plant culture Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping
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topic_title	SB1-1110 Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping wild rice grain length BSA fine mapping gene cloning
topic	misc SB1-1110 misc wild rice misc grain length misc BSA misc fine mapping misc gene cloning misc Plant culture
topic_unstemmed	misc SB1-1110 misc wild rice misc grain length misc BSA misc fine mapping misc gene cloning misc Plant culture
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title	Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping
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title_full	Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping
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journal	Frontiers in Plant Science
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author_browse	Lan Wang Yang Liu Haiyan Zhao Yuebin Zheng Feng Bai Sicheng Deng Zhixiong Chen Jinwen Wu Xiangdong Liu
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title_sort	identification of qgl3.5, a novel locus controlling grain length in rice through bulked segregant analysis and fine mapping
callnumber	SB1-1110
title_auth	Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping
abstract	Grain length (GL) directly affects the yield and quality of rice. Very few cloned GL-related genes are applied in production because their yield-increasing effects are not obvious, and the overall regulatory networks underlying the associated processes remain poorly understood. DNA samples from two bulk DNA pools (L-pool and S-pool) and their parents (KJ01 and Huaye 3) were subjected to high-throughput sequencing. Using bulked segregant analysis (BSA), qGL3.5 was mapped to a 0.34-Mb “hotspot” region on chromosome 3 that contains 37 genes related to various traits. Then, qGL3.5 was mapped to the genomic interval between the flanking markers M2 and M3 using 2786 BC4F2 individuals. Because the region from B5 to B6 was not the associated region under BSA-seq analysis, qGL3.5 was narrowed down to the interval between B6 and M3, which spanned 24.0-kb. Of all 37 genes with non-synonymous single-nucleotide polymorphisms (SNPs) between KJ01 and Huaye 3 based on BSA-seq analysis, only one complete annotated gene, ORF18 (Gene ID: LOC_Os03g42790.1) was found. ORF18 encodes an IBR-RING zinc-finger-related protein, with one really interesting new gene (RING) and two in between ring finger (IBR) domains. The knockout of ORF18 derived from Huaye 3 using clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) editing technology increased the GL of the mutant by approximately 2.2 mm. The novel locus qGL3.5 negatively regulated GL by promoting elongation of the longitudinal cell of the grain outer glume. These results provide a new genetic resource for rice grain shape breeding and a starting point for the functional characterization of the wild rice GL gene.
abstractGer	Grain length (GL) directly affects the yield and quality of rice. Very few cloned GL-related genes are applied in production because their yield-increasing effects are not obvious, and the overall regulatory networks underlying the associated processes remain poorly understood. DNA samples from two bulk DNA pools (L-pool and S-pool) and their parents (KJ01 and Huaye 3) were subjected to high-throughput sequencing. Using bulked segregant analysis (BSA), qGL3.5 was mapped to a 0.34-Mb “hotspot” region on chromosome 3 that contains 37 genes related to various traits. Then, qGL3.5 was mapped to the genomic interval between the flanking markers M2 and M3 using 2786 BC4F2 individuals. Because the region from B5 to B6 was not the associated region under BSA-seq analysis, qGL3.5 was narrowed down to the interval between B6 and M3, which spanned 24.0-kb. Of all 37 genes with non-synonymous single-nucleotide polymorphisms (SNPs) between KJ01 and Huaye 3 based on BSA-seq analysis, only one complete annotated gene, ORF18 (Gene ID: LOC_Os03g42790.1) was found. ORF18 encodes an IBR-RING zinc-finger-related protein, with one really interesting new gene (RING) and two in between ring finger (IBR) domains. The knockout of ORF18 derived from Huaye 3 using clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) editing technology increased the GL of the mutant by approximately 2.2 mm. The novel locus qGL3.5 negatively regulated GL by promoting elongation of the longitudinal cell of the grain outer glume. These results provide a new genetic resource for rice grain shape breeding and a starting point for the functional characterization of the wild rice GL gene.
abstract_unstemmed	Grain length (GL) directly affects the yield and quality of rice. Very few cloned GL-related genes are applied in production because their yield-increasing effects are not obvious, and the overall regulatory networks underlying the associated processes remain poorly understood. DNA samples from two bulk DNA pools (L-pool and S-pool) and their parents (KJ01 and Huaye 3) were subjected to high-throughput sequencing. Using bulked segregant analysis (BSA), qGL3.5 was mapped to a 0.34-Mb “hotspot” region on chromosome 3 that contains 37 genes related to various traits. Then, qGL3.5 was mapped to the genomic interval between the flanking markers M2 and M3 using 2786 BC4F2 individuals. Because the region from B5 to B6 was not the associated region under BSA-seq analysis, qGL3.5 was narrowed down to the interval between B6 and M3, which spanned 24.0-kb. Of all 37 genes with non-synonymous single-nucleotide polymorphisms (SNPs) between KJ01 and Huaye 3 based on BSA-seq analysis, only one complete annotated gene, ORF18 (Gene ID: LOC_Os03g42790.1) was found. ORF18 encodes an IBR-RING zinc-finger-related protein, with one really interesting new gene (RING) and two in between ring finger (IBR) domains. The knockout of ORF18 derived from Huaye 3 using clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) editing technology increased the GL of the mutant by approximately 2.2 mm. The novel locus qGL3.5 negatively regulated GL by promoting elongation of the longitudinal cell of the grain outer glume. These results provide a new genetic resource for rice grain shape breeding and a starting point for the functional characterization of the wild rice GL gene.
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title_short	Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping
url	https://doi.org/10.3389/fpls.2022.921029 https://doaj.org/article/e359d4fc4f954e16825ceee832e46e6a https://www.frontiersin.org/articles/10.3389/fpls.2022.921029/full https://doaj.org/toc/1664-462X
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up_date	2024-07-03T21:16:37.778Z
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Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping

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